GEO series

Polyadenylation at RNA polymerase III loci underlies the accumulation of noncoding retrotransposons during herpesviral infection

GSE288677 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2025/03/10 Platform GPL34328

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: RNA polymerase III transcription-associated polyadenylation promotes the accumulation of noncoding retrotransposons during infectionProceedings of the National Academy of Sciences of the United States of America · 2025

Summary (written by the submitters)

The cellular accumulation of short non-coding RNAs (ncRNAs) transcribed by RNA Polymerase III (Pol III) is a hallmark of various cellular stressors and inflammatory-associated diseases. Yet, the mechanisms driving the accumulation of these RNAs are largely undefined. Infection with several DNA viruses is known to significantly alter the cellular Pol III transcriptome, leading to the induction of a class of non-coding retrotransposons known as short interspersed nuclear elements (SINE) and tRNA genes.

Read the full summary ↓

Here, we sought to define the mechanisms driving Pol III transcribed ncRNA abundance during viral infection, using the murine herpesvirus MHV68 as a model. Our findings reveal that while the expression of Pol III transcripts, such as the murine-specific family of B2 SINE ncRNAs and pre-tRNAs, significantly increase during MHV68 infection, Pol III genomic occupancy is enhanced at a much fewer subset of B2 SINE and tRNA genes. Using DNA motif analyses and a convolutional neural network (CNN) based model, we identified non-promoter sequence elements within B2 SINE genes that distinguish infection-induced loci. We found that infection-induced B2 SINE genes are enriched for signal sequences that confer polyadenylation, and endogenous B2 SINE ncRNA polyadenylation depends on mRNA cleavage and polyadenylation (CPSF) machinery. We discovered that mRNA CPSF components are recruited to sites of Pol III transcription in response to MHV68 infection in a manner dependent on Pol III occupancy. Chromatin-associated B2 SINE ncRNAs are also bound by the CPSF complex, suggesting an RNA-dependent, co-transcriptional polyadenylation of B2 SINE ncRNAs. This uncovers an inducible, coupled relationship between Pol III transcription and mRNA-like polyadenylation of ncRNAs. Also, CPSF recruitment to Pol III genes is not restricted to murine genomes but also occurs at human SINE and tRNA genes, suggesting that this previously unknown coupled relationship may be a widespread feature of Pol III transcription.

Published in

RNA polymerase III transcription-associated polyadenylation promotes the accumulation of noncoding retrotransposons during infection

Lari A, Shah SB, Mao X et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40768347 · doi:10.1073/pnas.2507186122

This dataset

Open GSE288677 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE288677_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1219054 and SRA study SRP561428. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40768347) ↗

Study design

18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8772925 NIH3T3, mock-treated, Polr3A (input)
GSM8772926 NIH3T3, MHV68-treated, Polr3A (input)
GSM8772927 NIH3T3, mock-treated, replicate 1, Polr3A (ChIP)
GSM8772928 NIH3T3, mock-treated, replicate 2, Polr3A (ChIP)
GSM8772929 NIH3T3, MHV68-infected, replicate 1, Polr3A (ChIP)
GSM8772930 NIH3T3, MHV68-infected, replicate 2, Polr3A (ChIP)
GSM8772931 NIH3T3, control siRNA, mock-treated, CPSF30 (input)
GSM8772932 NIH3T3, control siRNA, MHV68-infected, CPSF30 (input)
GSM8772933 NIH3T3, Brf1 siRNA, mock-treated, CPSF30 (input)
GSM8772934 NIH3T3, Brf1 siRNA, MHV68-infected, CPSF30 (input)
GSM8772935 NIH3T3, control siRNA, mock-treated, replicate 1, CPSF30 (ChIP)
GSM8772936 NIH3T3, control siRNA, MHV68-infected, replicate 1, CPSF30 (ChIP)
GSM8772937 NIH3T3, Brf1 siRNA, mock-treated, replicate 1, CPSF30 (ChIP)
GSM8772938 NIH3T3, Brf1 siRNA, MHV68-infected, replicate 1, CPSF30 (ChIP)
GSM8772939 NIH3T3, control siRNA, mock-treated, replicate 2, CPSF30 (ChIP)
GSM8772940 NIH3T3, control siRNA, MHV68-infected, replicate 2, CPSF30 (ChIP)
GSM8772941 NIH3T3, Brf1 siRNA, mock-treated, replicate 2, CPSF30 (ChIP)
GSM8772942 NIH3T3, Brf1 siRNA, MHV68-infected, replicate 2, CPSF30 (ChIP)

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